Advance Payment - Issue with Taxes

We have issue as described below.
e.g.
Sales order of 1,000.
Taxes (10%) making total = 1100.

Customer pays advance of 500.
We need to be able to charge 5% of advance paid amount (500) not the whole amount of 1000.

So customer should pay total 550. and balance should be 550.

Is this configuration possible in erpnext?

The way system works.
Sales Order Amount =1000
Tax = 10%
Total =1100.
Advance 500, balance 600.

I hope this is clear.

I have a doubt …sales order 1000 and tax = 10% means totally 1100 right ? Please correct me if I m wrong .

You are right